Biology subjects

Courdavault, V.

Publications and source records attributed to Courdavault, V..

7 recordsLinked to original sources

bioRxiv2026

Multiple Shifts from Peptide-Based to Metabolite-Based Venoms in Ants

Venom systems are key evolutionary innovations that have contributed to the ecological success of numerous animal lineages. In ants (Formicidae), venom exhibits an exceptional diversity in both chemical composition and delivery mechanisms. Here, we combine a synthesis of current knowledge on the evolution of ant venoms with new phylogenetic comparative analyses, integrating chemical, morphological, and phylogenetic data at the genus level. Comparative analyses across Formicidae support the hypothesis that peptide-rich venoms represent the ancestral condition in ants, as they are widely distributed across basal and derived lineages. Despite this ancestral state, we identify seven independent evolutionary transitions toward non-peptidic venom, occurring in major clades including Dolichoderinae, Formicinae, Stenammini, Solenopsidini, Crematogaster, Pheidole, and fungus-growing ants. Ancestral state reconstruction and tests of correlated evolution across 114 genera show that these seven shifts away from peptide-based venom were almost irreversible and tightly coupled with the loss of stinging capacity and a dietary shift away from predation. These transitions are consistently associated with profound morphological modifications of the venom apparatus, such as reduction or complete loss of the sting, or its transformation into non-injecting structures. Chemically, these systems are dominated by alkaloids, iridoids, formic acid, esters, and terpenoids. These repeated transitions reflect major ecological and evolutionary shifts. Lineages that rely less on individual predation and more on collective foraging or plant-based diets tend to exhibit reduced reliance on injectable peptide toxins. Instead, they favor metabolite-based venoms that can be co-opted from existing biochemical pathways and deployed in diverse ecological contexts. Conversely, peptide-rich venoms are retained in lineages subjected to strong selective pressures for rapid prey immobilization or defense against vertebrate predators. Overall, ants represent a unique model for understanding venom evolution, illustrating how shifts in chemistry, morphology, and ecological strategy can drive repeated and convergent innovations. Future integrative studies combining genomics, metabolomics, and functional assays will be essential to unravel the mechanisms underlying these transitions and their role in the extraordinary diversification of ants.

evolutionary biology↗

bioRxiv2026

FASTOP - Fast editing toolkit for top expression sites in yeast

Budding yeast Saccharomyces cerevisiae is a workhorse chassis for producing added food and agricultural compounds. However, building multi-enzymatic pathways for these chemicals often requires iterative genomic integration, underscoring the need for efficient, rapid genome-editing tools that can reliably target transcriptionally active chromosomal regions. In this study, to accelerate strain construction, we established a genome-editing toolkit to rapidly engineer eight loci, highly expressed hot-spots, but nonessential genomic sites suitable for stable pathway assembly. Our approach integrates three key design features: (i) selectable markers to enable rapid screening of edited cells, (ii) extended homology arms that leverage the yeast homology-directed repair machinery for robust genomic integration, and (iii) co-delivery of Cas9 and guide RNAs to promote efficient double-stranded DNA breaks at specific integration sites. The sequence independence of FASTOP relies on the release of integration cassettes from integrative vectors, mediated by restriction digestion at two flanking multiple-cutting sites in the integration module to minimize the risk of introducing sequence errors during PCR amplification of the integration cassettes. Following the introduction of a fluorescent reporter cassette, we observed high integration efficiencies across the target sites. We then integrated the biosynthetic pathway of plant-derived flavonoid naringenin into the hot-spots of the yeast genome using the FASTOP toolkit. Our results demonstrated that upon expressing the five essential genes in simple shake flask culture, naringenin production reached 505.7 mg/L, representing a significant (69-fold) increase over previously reported titers for comparable minimal heterologous pathways in S. cerevisiae. Together, the FATSOP toolkit provides a user-friendly platform for reliably modifying hot-spot loci to rapidly construct multi-enzymatic metabolic pathways in S. cerevisiae, while achieving high production levels for high-value food-relevant metabolites.

synthetic biology↗

bioRxiv2026

Geissoschizine scaffolding enzymes shape monoterpene indole alkaloid biosynthesis

For decades, medicinal plants have been an invaluable source of therapeutics for human health. Among plant specialized metabolites, monoterpene indole alkaloids (MIAs) display remarkable chemical diversity and potent bioactivities, including anticancer properties. While the biosynthetic pathways leading to major MIAs such as vincristine, vinblastine, and camptothecin have been extensively studied, the mechanisms regulating metabolic flux within these pathways remain poorly understood. Here, we uncover an unexpected regulatory layer in MIA biosynthesis involving medium-chain dehydrogenase/reductase (MDR) proteins. Using a combination of in vitro biochemical assays, pathway reconstitution in planta, protein-protein interaction analyses, and metabolic engineering in yeast, we show that specific MDRs do not function as classical catalysts but instead enhance both the activity and diversify the stereochemical outputs of geissoschizine synthase (GS). These proteins physically interact with GS and strictosidine {beta}-glucosidase (SGD), forming ternary complexes that likely facilitate substrate channeling of reactive intermediates. Importantly, introduction of these MDRs into engineered yeast strains leads to a dramatic increase in the production of geissoschizine, a central MIA precursor. Collectively, our findings reveal a previously unrecognized role for MDR proteins as regulators of metabolic flux and highlight their potential as powerful tools for metabolic engineering of valuable plant natural products.

plant biology↗

bioRxiv2025

Evolution of CYP71D as a driving force of the diversification of monoterpene indole alkaloid biosynthesis

Monoterpene indole alkaloids (MIAs) constitute a vast group of plant natural products synthesized within the Gentianales order. MIAs possess outstanding pharmacological properties that explain their wide use in the treatment of human diseases. These biological activities result from the complex structure of MIAs that originate from intricated biosynthetic pathways involving several enzyme families and notably cytochrome P450s. The early steps of MIA synthesis involve several P450s from the 71 clade, which catalyse the conversion of various reduced strictosidine aglycones into MIAs from the mavacurane, strychnane, akuammilane, sarpagane, and heteroyohimane groups. An extensive study of these P450 distribution in genomic resources reveals that they all belong to a single evolutionary lineage named GAS clade, restricted to the MIA producing Gentianales (Gelsemiaceae and Rauvolfioideae). A related but distinct P450 lineage (named sister GAS clade) was found in non-MIA producing Gentianales and species producing structurally distinct MIAs (Rubiaceae). Functional characterization of 36 members of the GAS clade revealed that these enzymes felt into four main groups of activity depending on substrate acceptance (ex: tetrahydroalstonine, geissoschizine, ajmalicine...) and the nature of the catalyzed reaction (aromatization, cyclisation). These characterizations also lead to the identification of a yohimbane aromatization activity for several of these P450s, increasing the number of MIA scaffolds associated with GAS activity to six. Lastly, the chronology of emergence of these GAS activities was assessed by using ancestral sequence reconstitution, establishing that the initial ancestor of the whole GAS clade exhibits a main alstonine synthase activity. Subsequent gene duplication events, combined with neofunctionalization, facilitated the progressive emergence of eight additional activities, variably distributed among the four GAS subgroups. This comprehensive enzyme characterization establishes the evolutionary trajectory of the GAS clade, demonstrating how its diversification has progressively shaped the chemical diversity of MIAs in Gentianales.

biochemistry↗

bioRxiv2024

Genome-based discovery of pachysiphine synthases in Tabernaemontana elegans

Plant specialized metabolism represents an inexhaustible source of active molecules, some of which have been used in human health for decades. Among these, monoterpene indole alkaloids (MIAs) include a wide range of valuable compounds with anticancer, antihypertensive, or neuroactive properties. This is particularly the case for the pachysiphine derivatives which show interesting antitumor and anti-alzheimer activities but accumulate at very low levels in several Tabernaemontana species. Unfortunately, genome data in Tabernaemontanaceae are lacking and knowledge on the biogenesis of pachysiphine-related MIAs in planta remains scarce, limiting the prospects for biotechnological supply of many pachysiphine-derived biopharmaceuticals. Here, we report a raw version of the toad tree (Tabernaemontana elegans) genome sequence. These new genomic resources led to the identification and characterization of a couple of genes encoding cytochrome P450 with pachysiphine synthase activity. Our phylogenomic and docking analyses highlights the different evolutionary processes that have been recruited to epoxidize the pachysiphine precursor tabersonine at a specific position and in a dedicated orientation, thus enriching our understanding of the diversification and speciation of the MIA metabolism in plants. These gene discoveries also allowed us to engineer the synthesis of MIAs in yeast through the combinatorial association of metabolic enzymes resulting in the tailor-made synthesis of non-natural MIAs. Overall, this work represents a step forward for the future supply of pachysiphine-derived drugs by microbial cell factories. Significance StatementWhile pachysiphine is a monoterpene indole alkaloid of high interest and the precursor of an anti-Alzheimer compound, its biosynthesis involving the epoxidation of tabersonine remains uncharacterized. By sequencing and assembling the genome of Tabernaemontana elegans, we identified two P450s exhibiting a pachysiphine synthase activity that we modelized to explore the evolutionary scenario leading to the acquisition of this expoxidase activity; and used to engineer yeast cell factories for securing pachysiphine supply and producing new-to-nature alkaloids.

plant biology↗

bioRxiv2023

Rho of plant GTPases with geranylgeranylation motif modulate monoterpene indole alkaloid biosynthesis in Catharanthus roseus

Rho Of Plant (ROP) GTPases function as molecular switches that control signaling processes essential for growth, development, and defense. However, their role in specialized metabolism is poorly understood. Previously, we demonstrated that inhibition of protein geranylgeranyl transferase (PGGT-I) negatively impacts the biosynthesis of monoterpenoid indole alkaloids (MIA) in Catharanthus roseus, indicating the involvement of prenylated proteins in signaling. Here, we show through biochemical, molecular and in planta approaches that specific geranylgeranylated ROPs modulate C. roseus MIA biosynthesis. Among the six C. roseus ROP GTPases (CrROPs), only CrROP3 and CrROP5, having a C- terminal CSIL motif, were specifically prenylated by PGGT-I. Additionally, both of their transcripts showed higher expression in most parts compared to other CrROPs. Protein- protein interaction studies revealed that both CrROP3 and CrROP5, but not CrROP2 (lacking CSIL motif), interacted with CrPGGT-I. Further, CrROP3 and CrROP5 exhibited nuclear localization, whereas CrROP2 was localized to plasma membrane. In planta functional studies revealed that silencing of CrROP3 and CrROP5 negatively affected MIA biosynthesis, while their overexpression upregulated MIA formation. In contrast, silencing and overexpression of CrROP2 had no effect on MIA biosynthesis. Moreover, overexpression of {Delta}CrROP3 and {Delta}CrROP5 mutants lacking the CSIL motif failed to enhance MIA biosynthesis. Taken together, these results implicate that CrROP3 and CrROP5 have positive regulatory role on MIA biosynthesis and thus shed light on how geranylgeranylated ROP GTPases mediate the modulation of specialized metabolism in C. roseus.

plant biology↗

bioRxiv2018

Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks

Co-expression networks are essential tools to infer biological associations between gene products and predict gene annotation. Global networks can be analyzed at the transcriptome wide scale or after querying them with a set of guide genes to capture the transcriptional landscape of a given pathway in a process named Pathway Level Correlation (PLC). A critical step in network construction remains the definition of gene co-expression. In the present work, we compared how Pearson Correlation Coefficient (PCC), Spearman Correlation Coefficient (SCC), their respective ranked values (Highest Reciprocal Rank (HRR)), Mutual Information (MI) and Partial Correlations (PC) performed on global networks and PLCs. This evaluation was conducted on the model plant Arabidopsis thaliana using microarray and differently pre-processed RNA-seq datasets. We particularly evaluated how dataset x distance measurement combinations performed in 5 PLCs corresponding to 4 well described plant metabolic pathways (phenylpropanoid, carbohydrate, fatty acid and terpene metabolisms) and the cytokinin signaling pathway. Our present work highlights how PCC ranked with HRR is better suited for global network construction and PLC with microarray and RNA-seq data than other distance methods, especially to cluster genes in partitions similar to biological subpathways.

bioinformatics↗